How bacterial infections of the reproductive tract cause infertility and the correlation between the health status of female dogs and the presence of Mycoplasma canis (M. canis) in the vagina are still unclear. The aim of this study was to determine the M. canis population in the vagina of breeding bitches and to correlate this microbial population with some fertility outcomes. A total of 275 breeding bitches were included in the study. Vaginal samples were collected for microbiological and PCR testing. Mycoplasma canis was identified in 34.91% of the samples. One-third of bitches from the problem-free group and 41.18% from the group with problems were positive. In general, there were no significant differences in the prevalence of M. canis between the groups (P-value > 0.05). Mycoplasma canis occurs in both mated and unmated bitches and was found in a large number of kennels (67%). There was a correlation between M. canis in the kennel and the incidence of single puppy deaths and low litter sizes. There was also some correlation between the presence of M. canis in the vagina with at least two other bacterial strains and reproductive disorders. Our results indicate that M. canis is part of the normal vaginal flora of breeding bitches, although a role for this bacterium in causing some reproductive disorders remains to be disproved.